RetrogeneDB ID: retro_mmus_3506

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:109001484..109002293(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081793
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Capg
• Ensembl ID: ENSMUSG00000056737
• Aliases: Capg, gCap39, mbh1
• Description: capping protein (actin filament), gelsolin-like [Source:MGI Symbol;Acc:MGI:1098259]

Sequence

>retro_mmus_3506
CTGTACACACCCATCCCTAAGAGAGATTCTCCGCGGTTCCCAGCCTGAGTCCCAGATCCAGGCCTACACATATGGCCTGT
GGAGAAGCTGAAGCCAGTGCCCATAGCAAGAATGAACCATGGCATCTTTTTCTCTGGGTATTCCTACCTAGTGTGTCACA
AGGCCCAGAAGAGGCCTCCCATCTGCACCTGAGGATAGGCCAGCAGTCATCCTGAAAGGAGCAGGGGGCCTGTGCTCTGC
TGGCTGAGAACCTCAACACCATGCTGGGAGAGCAGACTGTGCAGCGTCCTGTGCAGCGCCCTGAGGGTCAAGAGAATAAA
TCTGACCTCTTCATGAATTACTTCCCATGAGGCCTCAAGTACCGGGAAGGTGGCGTGGAGTTGGCATTTCACCAGACAAC
CTCGAGCGCCACCCCAGCAGCCATCAGGAAGCTCTACCAGGTTAAGGGTAAGAACATCTGTGTGACCGAGAGGGCTCTGA
GCTGGGACAGCTTCAACACTGGGGACTGCTTCATCCTGGACCTGGGTCTGAACATCTTTGCCTGGTGTGGTAGAAAGTCG
GATATCCTGGAGCGCAACAAGGCGAGGGACCTGGCACTGGCCATCAGGGACAGCGAATGGCAGGGCAAGGCCCAGGTGGA
AATCATTACTGATGGAGAGGAGCCAGCTGAGATGATTCTAGGCCCCAAGCCTGCTCCAAAGGAGGGTAACCCTGAGGAAG
ACATTACAGCTGACCAGACCAAGGCTCAGGCGGCAGCCGCGTATAAGGTCTCTGATGCCACTGAACAGATGGATATGACC
AAGGTGGCT

Alignment

ORF - retro_mmus_3506 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.39 %
• Parental protein coverage: 76.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MYTPIPQSGSP-FPASVQDPGLHIWRVEKLKPVPIARESHGIFFSGDSYLVLHN-GPEEASHLHLWIGQQ
          .YTPIP...SP.FPA.V.DPGLHIW.VEKLKPVPIAR..HGIFFSG.SYLV.H..GPEEASHLHL.IGQQ
Retrocopy LYTPIPKRDSPRFPA*VPDPGLHIWPVEKLKPVPIARMNHGIFFSGYSYLVCHK<GPEEASHLHLRIGQQ

Parental  SSRDEQGACAVLAVHLNTLLG----ERPVQHREVQGNESDLFMSYFPRGLKYREGGVESAFHKTTSGATP
          SS..EQGACA.LA..LNT.LG.....RPVQ..E.Q.N.SDLFM.YFP.GLKYREGGVE.AFH.TTS.ATP
Retrocopy SS*KEQGACALLAENLNTMLGEQTVQRPVQRPEGQENKSDLFMNYFP*GLKYREGGVELAFHQTTSSATP

Parental  AAIRKLYQVKGKKNIRATERALSWDSFNTGDCFILDLGQNIFAWCGGKSNILERNKARDLALAIRDSERQ
          AAIRKLYQVKGK.NI..TERALSWDSFNTGDCFILDLG.NIFAWCG.KS.ILERNKARDLALAIRDSE.Q
Retrocopy AAIRKLYQVKGK-NICVTERALSWDSFNTGDCFILDLGLNIFAWCGRKSDILERNKARDLALAIRDSEWQ

Parental  GKAQVEIITDGEEPAEMIQVLGPKPALKEGNPEEDITADQTNAQAAALYKVSDATGQMNLTKVA
          GKAQVEIITDGEEPAEMI..LGPKPA.KEGNPEEDITADQT.AQAAA.YKVSDAT.QM..TKVA
Retrocopy GKAQVEIITDGEEPAEMI--LGPKPAPKEGNPEEDITADQTKAQAAAAYKVSDATEQMDMTKVA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.02 RPM	1.43 RPM
SRP007412_cerebellum	0.00 RPM	1.82 RPM
SRP007412_heart	0.00 RPM	10.99 RPM
SRP007412_kidney	0.08 RPM	23.08 RPM
SRP007412_liver	0.03 RPM	5.16 RPM
SRP007412_testis	0.00 RPM	0.73 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3506 was not detected

EST

No EST(s) were mapped for retro_mmus_3506 retrocopy.

TSS

No TSS is located nearby retro_mmus_3506 retrocopy 5' end.

Lab

retro_mmus_3506 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3506 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019705	2 retrocopies	retro_cjac_3816, retro_cjac_459,
Macropus eugenii	ENSMEUG00000013559	1 retrocopy	retro_meug_1063,
Mus musculus	ENSMUSG00000056737	1 retrocopy	retro_mmus_3506 ,
Otolemur garnettii	ENSOGAG00000001084	1 retrocopy	retro_ogar_3277,
Rattus norvegicus	ENSRNOG00000013668	1 retrocopy	retro_rnor_840,